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Create auto_bioconda_pr.yaml
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‎.github/workflows/auto_bioconda_pr.yaml‎

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name: Auto Bioconda PR with Test & meta.yaml generation (Manual Only)
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on:
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workflow_dispatch:
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jobs:
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bioconda_pr:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout this repo
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uses: actions/checkout@v3
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- name: Extract version and package name using ast
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id: vars
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run: |
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set -e
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INIT_PATH=$(find . -type f -name '__init__.py' | head -n1)
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echo "📄 Found __init__.py at: $INIT_PATH"
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echo 'import ast' > get_version.py
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echo 'with open("'$INIT_PATH'") as f:' >> get_version.py
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echo ' tree = ast.parse(f.read())' >> get_version.py
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echo 'for node in ast.walk(tree):' >> get_version.py
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echo ' if isinstance(node, ast.Assign):' >> get_version.py
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echo ' if getattr(node.targets[0], "id", None) == "__version__":' >> get_version.py
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echo ' print(node.value.s)' >> get_version.py
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echo ' break' >> get_version.py
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VERSION=$(python3 get_version.py)
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PACKAGE=$(basename $(dirname "$INIT_PATH"))
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if [ -z "$VERSION" ]; then
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echo "❌ __version__ not found in $INIT_PATH"
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cat "$INIT_PATH"
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exit 1
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fi
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echo "📦 PACKAGE: $PACKAGE"
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echo "📌 VERSION: $VERSION"
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echo "VERSION=$VERSION" >> $GITHUB_ENV
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echo "PACKAGE=$PACKAGE" >> $GITHUB_ENV
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- name: Generate meta.yaml in recipes/${PACKAGE}
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run: |
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mkdir -p recipes/${PACKAGE}
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echo "{% set name = \"${PACKAGE}\" %}" > recipes/${PACKAGE}/meta.yaml
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echo "{% set version = \"${VERSION}\" %}" >> recipes/${PACKAGE}/meta.yaml
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echo "" >> recipes/${PACKAGE}/meta.yaml
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echo "package:" >> recipes/${PACKAGE}/meta.yaml
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echo " name: \"{{ name|lower }}\"" >> recipes/${PACKAGE}/meta.yaml
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echo " version: \"{{ version }}\"" >> recipes/${PACKAGE}/meta.yaml
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echo "" >> recipes/${PACKAGE}/meta.yaml
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echo "source:" >> recipes/${PACKAGE}/meta.yaml
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echo " url: https://github.com/kamome1201/${PACKAGE}/archive/refs/tags/v{{ version }}.tar.gz" >> recipes/${PACKAGE}/meta.yaml
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echo " sha256: \"TO_BE_REPLACED\"" >> recipes/${PACKAGE}/meta.yaml
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echo "" >> recipes/${PACKAGE}/meta.yaml
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echo "build:" >> recipes/${PACKAGE}/meta.yaml
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echo " number: 0" >> recipes/${PACKAGE}/meta.yaml
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echo " noarch: python" >> recipes/${PACKAGE}/meta.yaml
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echo " script: \"{{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps\"" >> recipes/${PACKAGE}/meta.yaml
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echo "" >> recipes/${PACKAGE}/meta.yaml
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echo "requirements:" >> recipes/${PACKAGE}/meta.yaml
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echo " host:" >> recipes/${PACKAGE}/meta.yaml
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echo " - python >=3.8" >> recipes/${PACKAGE}/meta.yaml
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echo " - pip" >> recipes/${PACKAGE}/meta.yaml
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echo " - setuptools" >> recipes/${PACKAGE}/meta.yaml
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echo " - wheel" >> recipes/${PACKAGE}/meta.yaml
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echo " run:" >> recipes/${PACKAGE}/meta.yaml
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echo " - python >=3.8" >> recipes/${PACKAGE}/meta.yaml
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echo "" >> recipes/${PACKAGE}/meta.yaml
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echo "test:" >> recipes/${PACKAGE}/meta.yaml
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echo " imports:" >> recipes/${PACKAGE}/meta.yaml
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echo " - ${PACKAGE}" >> recipes/${PACKAGE}/meta.yaml
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echo "" >> recipes/${PACKAGE}/meta.yaml
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echo "about:" >> recipes/${PACKAGE}/meta.yaml
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echo " home: \"https://github.com/kfuku52/${PACKAGE}\"" >> recipes/${PACKAGE}/meta.yaml
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echo " license: \"BSD-3-Clause\"" >> recipes/${PACKAGE}/meta.yaml
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echo " license_file: \"LICENSE\"" >> recipes/${PACKAGE}/meta.yaml
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SUMMARY=$(head -n 1 README.md | sed 's/"/\\"/g')
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echo " summary: \"${SUMMARY}\"" >> recipes/${PACKAGE}/meta.yaml
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- name: Download source archive and compute SHA256
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run: |
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url="https://github.com/kamome1201/${PACKAGE}/archive/refs/tags/v${VERSION}.tar.gz"
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wget -O source.tar.gz "$url"
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sha256=$(sha256sum source.tar.gz | awk '{print $1}')
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echo "SHA256=$sha256" >> $GITHUB_ENV
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echo "SHA256=$sha256" # ← ログ確認用に追加
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- name: Clone your fork of bioconda-recipes
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run: |
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git clone https://github.com/kamome1201/bioconda-recipes.git
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cd bioconda-recipes
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git remote add upstream https://github.com/bioconda/bioconda-recipes.git
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git fetch upstream
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- name: Create new branch
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run: |
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cd bioconda-recipes
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git checkout -b add-${PACKAGE}-${VERSION}
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- name: Copy recipe into bioconda-recipes
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run: |
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cp -r recipes/${PACKAGE} bioconda-recipes/recipes/
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- name: Replace sha256 in meta.yaml
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run: |
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sed -i "s/sha256: .*/sha256: \"${{ env.SHA256 }}\"/" bioconda-recipes/recipes/${PACKAGE}/meta.yaml
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- name: Create config.yml for bioconda-utils
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run: |
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echo "channels:" > bioconda-recipes/config.yml
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echo " - bioconda" >> bioconda-recipes/config.yml
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echo " - conda-forge" >> bioconda-recipes/config.yml
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echo " - defaults" >> bioconda-recipes/config.yml
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- name: Check copied recipe contents
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run: |
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ls -R bioconda-recipes/recipes
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- name: Run lint + build + test with bioconda-utils (Docker)
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run: |
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ABS_PATH=$(realpath bioconda-recipes)
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docker run --rm -v $ABS_PATH:/bioconda-recipes \
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quay.io/bioconda/bioconda-utils-build-env \
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bioconda-utils build recipes config.yml --packages ${PACKAGE} --loglevel info --docker --git-range master
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# - name: Commit and push
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# run: |
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# cd bioconda-recipes
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# git add recipes/${PACKAGE}
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# git commit -m "Update ${PACKAGE} recipe to v$VERSION"
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# git push origin add-${PACKAGE}-${VERSION}
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# - name: Create Pull Request
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# uses: peter-evans/create-pull-request@v5
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# with:
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# token: ${{ secrets.GH_PAT }}
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# title: "Update ${PACKAGE} recipe to v${{ env.VERSION }}"
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# commit-message: "Auto PR for Bioconda: ${PACKAGE} v${{ env.VERSION }}"
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# base: master
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# branch: add-${PACKAGE}-${{ env.VERSION }}
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# body: |
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# This PR was automatically generated by GitHub Actions.
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# - Package: ${{ env.PACKAGE }}
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# - Version: v${{ env.VERSION }}
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# - sha256: ${{ env.SHA256 }}

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